DNAH3 p.Asn1759=
c.5277C>T · rs114086288 · VCV776991
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 3.08%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.1 | GERP -0.88, phastCons 1 |
| Overall | ||
| CADD | 4.238 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.08%
African / African-American · 2,311/75,004 alleles
Filtering AF
2.98%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.93%
Overall
0.167%
2,689/1,614,116 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.08% | 32 |
| Admixed American | 0.235% | 426 |
| Middle Eastern | 0.214% | 466 |
| Remaining individualsnot grpmax-eligible | 0.182% | 548 |
| South Asian | 0.0132% | 7,590 |
| European (non-Finnish) | 0.0083% | 12,041 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- DNAH3
- Protein
- p.Asn1759=
- Coding
- c.5277C>T
- MANE Select
- NM_001347886
- dbSNP
- rs114086288
- Type
- single nucleotide variant
- Location
- chr16:21031069 (GRCh38)
- Gene constraint
- LOEUF 0.834 · pLI <0.01 (gnomAD)
- Residue 1759
- a UniProt-annotated variant site (found in a male with oligoasthenoteratozoospermia; uncertain significance; severely impaired sperm motility; multiple morphological abnormalities of the sperm flagella; partial loss and disintegration of the flagellar axoneme, accompanied by damage to the mitochondrial sheath); the 'aaa 2' region
Similar variants
- DNAH3 p.Ala1918Gly Uncertain significance ★★ ⚠ same type
- DNAH3 p.Arg1228Gln Uncertain significance ★★ same type
- DNAH3 p.Arg635Gln Uncertain significance ★★ same type
- DNAH3 p.Asn1728Ser Uncertain significance ★★ ⚠ same type
- DNAH3 p.Asp3656Asn Uncertain significance ★★ same type
- DNAH3 p.Leu2597Val Uncertain significance ★★ same type
- DNAH3 p.Leu4044Phe Uncertain significance ★★ ⚠ same type
- DNAH3 p.Lys374Gln Uncertain significance ★★ ⚠ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/dnah3-p-asn1759 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown